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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGGCAGTAGCCATGGGCATCCTGGACCACCTGTCGCATCTGTGCAGCATCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatggtatgagagctagctgcttgctgctgcctcctgctgctgctagctgctgctttgtctcttgattcgcgcgctgcatgccatggttgcttggcag

Basic information

species Zea mays
transcript GRMZM2G104041_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104041_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g32330.1 (Oryza sativa), 5'ss of exon 1
AGCGGCAGTAGCCATGGGCATCCTGGACCACCTGTCGCATCTGTGCAGCATCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatggtatgagagctag--ctgcttgctgctgcctcctgc-tgc-tgctagctgctgctttgtctcttgattcgcgcgctgcatgccatggttgcttggcag---------------------------------------------------------------
|  |  || | |||||||  |  |||||  ||| ||  || |||||||| | || ||||| ||||| || |||||||| |||||||||||||| ||||||||    ||   |    || || |  |   ||     | |  | ||| ||| || | |||     || ||    | |||   || | |      ||   |   ||                                                                   
ACAGAGAGCAACCATGGGTGTATTGGACAGCCTCTCTGATATGTGCAGCCTGACAGAGACCAAGGAAGCCCTCAAGCTAAGGAAGAAGCGGCCACTGCAGgtgttttaattttctcgatcttgatcgatttatatatactacatgcatgcatgtttgctcaaatttcgttggctaattaa-gcacagagataaattaatttgtgaagttcttgtgcttcttcattaattaatttggtgatgtgtttttgcttatacaatatgtgtgtgtag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211481808|gb|FL154366.1|FL154366
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAG                         ACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatg ... tgcttggcagACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
EST: gi|211205520|gb|FL437991.1|FL437991
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAG                         ACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatg ... tgcttggcagACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
EST: gi|13558348|gb|BG549704.1|BG549704
EST:     AGGCGCTCAAGCTCA-GAAGAAGCGGCCGCTGCAG                         ACTG-GAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
genomic: AGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatg ... tgcttggcagACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
EST: gi|211481804|gb|FL154362.1|FL154362
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAG                         ACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatg ... tgcttggcagACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
EST: gi|13558715|gb|BG550071.1|BG550071
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAG                         ACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatg ... tgcttggcagACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
EST: gi|211481807|gb|FL154365.1|FL154365
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAG                         ACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGC
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatg ... tgcttggcagACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGC
EST: gi|211478925|gb|FL154356.1|FL154356
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAG                         ACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatg ... tgcttggcagACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
EST: gi|211478927|gb|FL154358.1|FL154358
EST:     TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGACCGCTGCAG                         ACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG
genomic: TCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatg ... tgcttggcagACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 16 (upstream exon), 47 (downstream exon)
Score: 7

AGCGGCAGTAGCCATGGGCATCCTGGACCACCTGTCGCATCTGTGCAGCATCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatg ... tgcttggcagACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTGAAGAGCGCGGTGAAGTCGATGCGCGGCGTGACGAGCGTGGCGGTGAACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 57

AGCGGCAGTAGCCATGGGCATCCTGGACCACCTGTCGCATCTGTGCAGCATCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatg ... tgcttggcagACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTGAAGAGCGCGGTGAAGTCGATGCGCGGCGTGACGAGCGTGGCGGTGAACG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 7

AGCGGCAGTAGCCATGGGCATCCTGGACCACCTGTCGCATCTGTGCAGCATCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatg ... tgcttggcagACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTGAAGAGCGCGGTGAAGTCGATGCGCGGCGTGACGAGCGTGGCGGTGAACG


Block sizes: 31 (upstream exon), 47 (downstream exon)
Score: 18

AGCGGCAGTAGCCATGGGCATCCTGGACCACCTGTCGCATCTGTGCAGCATCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatg ... tgcttggcagACTGTGAACATCAAGGTGAAGATGGACTGCGAAGGGTGCGAGCGCCGCGTGAAGAGCGCGGTGAAGTCGATGCGCGGCGTGACGAGCGTGGCGGTGAACG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGGCAGTAGCCATGGGCATCCTGGACCACCTGTCGCATCTGTGCAGCATCACGGAGACGAAGGAGGCGCTCAAGCTCAGGAAGAAGCGGCCGCTGCAGgtacggtatggtatgagagctagctgcttgctgctgcctcctgctgctgctagctgctgctttgtctcttgattcgcgcgctgcatgccatggttgcttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG